Man, all this time and you guys forgot one of the most important factors for extremely weak Pok?mon?
Well, I'll get to that in a moment. There are many factors that would determine that battle. As people have said before, it depends on level, nature, and stats. Nowadays, since Poison type moves are now not considered super-effective against Bug type Pok?mon, I'd say that Metapod would win. Assuming that both Pok?mon have identical stats and/or levels, Metapod's Tackle has a power of 40, whereas Kakuna's Poison Sting has a total power of 22.5 because of it's type combatabilities. Overall, Metapod should do more damage considering that it can outdo Kakuna's attack, even if it misses once or twice. Poison probably wouldn't too much damage to Metapod because of it's Shed Skin ability. Of course, that depends on its level.
Well, besides these two cacoon Pok?mon who can't move around much until they evolve, what about Silcoon and Cascoon? Shouldn't they be a part of this?
And why in the world would Team Rocket steal any of them? I'm pretty sure they're not all too interested in Butterfree, had quite enough of Beedril, despise Beautifly because of May's, and they already have a Dustox.
Of course, Metapod's, Kakuna's, Silcoon's, and Cascoon's attacks really, REALLY stink! If you want to quickly determine the winnner of any of those battles, make sure none of them have any PP left in their moves. And when you do battle, then they become quite the battler with Struggle! It's the stongest move any of them can get while in their hardened state! The battle should go rather quickly, so it's very easy to determine who'd win! (I wouldn't know...)